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Gene

H3-3A

H3.3 histone A

Summary

Cytogenetic location
1q42.12
Coordinates
Chromosome 1: 226,062,716–226,072,019 (GRCh38)
Exons
4 exons across 9.3 kb
Protein
136 amino acids
Also known as
H3.3A
Previous symbols
H3F3, H3F3A
MANE Select transcript
ENST00000366815.10NM_002107.7
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

No Genome Test report reads H3-3A yet. The test sequences your whole genome, so your data includes it all the same.

How H3-3A is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 1, with a bracket where H3-3A sits. H3-3A and 14 genes near it on chromosome 1, from 225,567,368 to 226,567,367.Chromosome 11q42.12p36.33p36.32p36.31p36.23p36.22p36.21p36.13p36.12p36.11p35.3p35.2p35.1p34.3p34.2p34.1p33p32.3p32.2p32.1p31.3p31.2p31.1p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q21.1q21.2q21.3q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q31.1q31.2q31.3q32.1q32.2q32.3q41q42.11q42.12q42.13q42.2q42.3q43q44225.6 Mb225.8 Mb226 Mb226.2 Mb226.4 MbENAH: 225,486,765–225,653,334, reverse strandENAHSRP9: 225,777,699–225,790,670, forward strandSRP9EPHX1: 225,810,048–225,845,567, forward strandEPHX1TMEM63A: 225,845,532–225,884,122, reverse strandTMEM63ALEFTY1: 225,886,279–225,911,382, reverse strandLEFTY1: 225,886,696–225,924,278, reverse strandPYCR2: 225,914,982–225,924,340, reverse strandPYCR2LEFTY2: 225,936,598–225,941,532, reverse strandLEFTY2SDE2: 225,982,693–225,999,385, reverse strandSDE2H3-3A: 226,062,716–226,072,019, forward strandH3-3AACBD3: 226,144,679–226,186,763, reverse strandACBD3MIXL1: 226,223,508–226,227,384, forward strandMIXL1LIN9: 226,231,149–226,309,869, reverse strandLIN9PARP1: 226,360,210–226,408,154, reverse strandPARP1STUM: 226,548,714–226,609,230, forward strandSTUMDiagram of H3-3A: 4 exons on the forward strand of chromosome 1Exon 2: 1 known disease-causing siteExon 3: 4 known disease-causing sitesExon 4: 6 known disease-causing sitesExon 1: 226,062,716–226,062,811, 96 basesExon 2: 226,064,329–226,064,479, 151 basesExon 3: 226,065,656–226,065,809, 154 basesExon 4: 226,071,351–226,072,019, 669 bases12345′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 1.1 kb of the gene's 9.3 kb; 411 of those bases code for the protein.

How a genome test reads H3-3A

11

positions in H3-3A where ClinVar classes a change as pathogenic or likely pathogenic

8 of them (73%) fall in regions short reads find hard.

  • Low mappability (8 sites)Regions where 100 bp or 250 bp reads cannot be placed uniquely.

A whole genome covers all 9.3 kb of H3-3A, introns included, not only the 1.1 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). H3-3A gene: H3.3 histone A. Retrieved 17 October 2026, from https://dantelabs.com/genes/h3-3a

Vancouver

Dante Labs. H3-3A gene: H3.3 histone A [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/h3-3a

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